We are going to take stronger measures against harmful diseases, and that reduces their fitness inevitably. The claim that a disease always evolves towards being more harmless is obviously not true due to mere chance, but in the long run there is a clear advantage to it. Rather than cherry-picking examples to prove the point I think it's more accurate to say the article cherry-picks counterexamples like multiple Malaria strands competing against each other in the same host or a rabbit disease that became more deadly to overcome an immune response. None of which is long-term adaptive.